Naryn basin, which has the largest river catchment area in Kyrgyz Republic and many mountain glaciers, is a huge ‘water tower’ for Kyrgyz Republic and Uzbekistan. Thus, the behavior of its glaciers has a large impact on water resources for the arid flat plain below, providing water for residents, irrigation, and energy in Kyrgyz Republic and Central Asia. We investigated the recent glacier condition in the Naryn basin (Chon Naryn and Kichi Naryn catchments) using topographic maps of 1:25,000 scale and ALOS/AVNIR-2 satellite imagery. For the 45-year period 1965–2010, glacier area decreased by 17.4% in the Akshyirak massif, and by 20.8% in the Borkoldoy, 21.9% in the Jetim, 24.6% in the Jetimbel, 28.9% in the Naryn, 20.8% in the Sook, 20.9% in the Teskey (south-slope glaciers), and 17.8% in the Uchemchek mountain ranges. The dramatic shrinkage was greater for south-facing than for north-facing glaciers, with respective area losses of 23.6 and 19.8%. The glacier shrinkage might affect not only irrigation water withdrawals during summer but also the planning of four cascade power stations to be constructed in the Chon Naryn and Kichi Naryn catchments.